IUBio GIL .. BIOSCI/Bionet News .. Biosequences .. Software .. FTP

lookup and SRS5, part two

Guy Bottu gbottu at ben.vub.ac.be
Tue Jul 8 07:30:41 EST 1997

I am trying to make lookup work with the indexes of SRS5. I am however
afraid it won't work. I have already discovered the following :

lookup can find entries correctly in the indexes made by SRS5, provided
the short name is the same. The only name that changed between the
distributions of GCG8/SRS4 and SRS5 is Definition(DEF) -> Description
(DES). Replacing Definition and DEF in the source code of lookup by
Description and DEF and recompiling does not help, lookup still does not
retrieve anything. There is however an easy getaround : it is sufficient
to make UNIX logical links from embl_def.ids to embl_des.ids,... to make
it work. 

It goes wrong however when you ask for the output. The entry names of
the retrieved sequences are correct, but you get often a wrong
definition and database name (e.g. EM_OR instead of EM_VI) or an error
message "* ERROR * end of file encountered". Has the format of the index
*_id.idx that points to the location of the databank entries changed ?

	Guy Bottu

this message has also been posted to : bionet.software.gcg

More information about the Bio-srs mailing list

Send comments to us at archive@iubioarchive.bio.net